RNA structure determines function.
Each RNA molecule is made up of a sequence of individual units, nucleotides (bases), which are of four common types, A, U, G and C
(Figure REF ).
Individual RNA sequences range in length from tens (tRNAs, siRNAs) to tens of thousands (viral genomes, long non-coding RNAs) and many contain further chemical modifications of the individual bases [1]}.
While identity is defined by sequence, the function of an RNA molecule is determined by its structure, i.e., the way nucleotides interact in space.
Biochemists often break down RNA structure into four categories: (1) Primary structure refers to the sequence. (2) Secondary structure makes up the majority of the bonds in the structure and includes the “canonical base pairs”, where A pairs with U and G pairs with C, and the “wobble base pair”, where G pairs with U. This provides a 2D representation of the structure of the molecule and is the most commonly used level. (3) Tertiary structure defines 3D contacts via weaker, non-conical interactions. (4) Finally quaternary structure includes intermolecular interactions with other RNA molecules. Given the impact of structure on RNA functionality, the accurate computational prediction of the secondary and tertiary structure of RNA is an ongoing area of great interest in the computational biology community [2]}, [3]}.
